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WO2019008093A1 - Marqueurs pour diagnostiquer des maladies intestinales inflammatoires - Google Patents

Marqueurs pour diagnostiquer des maladies intestinales inflammatoires Download PDF

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Publication number
WO2019008093A1
WO2019008093A1 PCT/EP2018/068244 EP2018068244W WO2019008093A1 WO 2019008093 A1 WO2019008093 A1 WO 2019008093A1 EP 2018068244 W EP2018068244 W EP 2018068244W WO 2019008093 A1 WO2019008093 A1 WO 2019008093A1
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seq
markers
group
subject
expression
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PCT/EP2018/068244
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English (en)
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Albin Gustav SANDELIN
Mette BOYD
Malte THODBERG
Morana VITEZIC
Jette BORNHOLDT LANGE
Kristoffer VITTING-SEERUP
Jacob BJERRUM
Ole HAAGEN NIELSEN
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University Of Copenhagen
Region Hovedstaden V/Herlev Hospital
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Publication of WO2019008093A1 publication Critical patent/WO2019008093A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to genomic regions which are useful markers for determining whether a subject suffers from an inflammatory bowel disease, such as ulcerative colitis or Crohn's disease, or is healthy. Also disclosed are useful primers for measuring expression levels of said markers, as well as computer-implemented methods.
  • IBD Inflammatory bowel disease
  • UC ulcerative colitis
  • CD Crohn's disease
  • IBDs ulcerative colitis or Crohn's disease
  • diagnosis of IBDs is based on visual inspection of the gut through endoscopy, and histology assessment of pinch biopsies taken in the same colonoscopy, but can it also include radiology, x-ray and microbiology-based methods. These methods are time-consuming and assessment of the symptoms can be subjective. There is a need for easier methods which are quantitative and reliable, i.e. having high specificity, sensitivity and accuracy, and which can be performed routinely. Summary
  • RNA profiling method that sequences the 5' ends of RNAs (CAGE) was applied on biopsies from the descending colon from 94 IBD patients and controls, providing a genome-wide map of transcription start sites (TSSs) across individuals with and without IBD. From this set, we identified TSSs that diagnose inflammatory bowel diseases such Crohn's disease or ulcerative colitis with an accuracy of 85%, using qPCR to measure RNA expression, where the prediction method was trained on one cohort and evaluated in another independent cohort. Provided herein are improved methods for diagnosing IBD and particularly for discriminating between UC and CD with a high level of accuracy. Correct diagnosis of IBD patients is important since the treatments for UC and CD are not the same.
  • a method of diagnosing an inflammatory bowel disease comprising the steps of
  • markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91 , SEQ ID NO:
  • transcripts optionally extracting transcripts from the first and the second samples; (iv) measuring and comparing the levels of at least part of the first set of transcripts and at least part of the second set of transcripts;
  • transcripts at least part of the second set of transcripts and at least part of the third set of transcripts;
  • transcripts at least part of the second set of transcripts and at least part of the third set of transcripts;
  • kit of parts comprising:
  • - optionally a software for diagnosing an inflammatory bowel disease, Crohn's disease or ulcerative colitis.
  • the markers are as defined in any one of the preceding claims, and wherein the expression profile represents the expression levels of the at least 2 markers together in said subject, the first expression signature represents the average expression levels of the at least 2 markers together in a group of at least 20 healthy subjects, and the second expression signature represents the average expression levels of the at least 2 markers together in a group of subjects suffering from an inflammatory bowel disease;
  • the method determines that the subject is healthy
  • determining that the subject suffers from an inflammatory bowel disease Also provided is a computer implemented method for automatically determining whether a subject suffers from ulcerative colitis or from Crohn's disease, the method comprising the steps of:
  • the expression profile represents the expression levels of the at least 2 markers together in said subject
  • the first reference profile represents the average expression levels of the at least 2 markers together in a group of at least 20 healthy subjects
  • the second reference profile represents the average expression levels of the at least 2 markers together in a group of subjects suffering from ulcerative colitis
  • the third reference profile represents the average expression levels of the at least 2 markers together in a group of subjects suffering from
  • Figure 1 defining the TSS landscape of IBD: Overview of human subject datasets used for selection of biomarkers/features (cohort 1) and independent validation (cohort 2).
  • cohort 1 pinch biopsies from the descending colon were taken from 94 human subjects, classified into active ulcerative colitis (UCa), active Crohn's disease (CDa), UC and CD patients in remission (UCi, CDi) and controls (Ctrl: subjects screened for IBD where all subsequent investigations turned out normal.
  • UCa active ulcerative colitis
  • CDa active Crohn's disease
  • CDi UC and CD patients in remission
  • Ctrl subjects screened for IBD where all subsequent investigations turned out normal.
  • TSSs transcription start sites
  • Schematics show the typical inflammatory patterns in the intestinal system, the approximate location of biopsy sampling and number of subjects in each group.
  • FIG. 3 Classification of IBD subtypes and controls.
  • Figure 4 Prediction of UCa/CDa/Ctrl diagnosis labels based on CAGE expression data.
  • CAGE RNA expression data from cohort 1 from 263 selected features was used to train and evaluate a Random Forest prediction method based on 5-fold cross- validation.
  • Left panel average accuracy, sensitivity and specificity are shown for each subject group as bar plots along with the overall accuracy. Error-bars show 95% confidence intervals.
  • Right panel confusion matrix showing the average fractions of predictions that fall into each of the actual subject groups (columns add to 100% of predictions).
  • Lower panel Average prediction accuracy (Y-axis) as a function of the number of features used for training the Random Forests (X-axis) for predicting CD,
  • Figure 5 Prediction of UCa/CDa/Ctrl diagnosis labels based on microfluidics qPCR expression data. Plots are organized as in figure 4, but based on microfluidics qPCR RNA expression data from cohort 1 using 161 primers corresponding to the selected features.
  • Feature reduction based on the data in panel C resulted in the selection of 35 features with corresponding primers.
  • the upper right panel shows a comparison between the confusion matrix of the predictions and the confusion matrix obtained by repeating the analysis with randomly shuffled UCa, CDa and Ctrl training labels. Numbers indicate the average fold changes of actual vs. shuffled data.
  • An xgBoost model was trained on microfluidic qPCR data from the 35 biomarkers from cohort 1 and evaluated it on corresponding data from an independent cohort (cohort 2).
  • Upper panel average accuracy, sensitivity and specificity are shown for each subject group as bar plots along with overall accuracy. Error-bars show 95% confidence intervals across cross-validations. Dotted lines indicate 0.8 and 0.9.
  • Lower left panel confusion matrix showing average fractions of predictions that fall into each of the actual subject groups (columns add to 100%).
  • Lower right panel shows a comparison between the confusion matrix (as in panel b) of the predictions and the confusion matrix obtained by repeating the analysis with randomly shuffled training labels. Numbers indicate the average fold changes of fractions (actual vs. shuffled).
  • Figure 7 Ranking of selected makers for UCa vs. CDa .
  • 1000 random forests were trained to distinguish UCa vs. CDa.
  • the importance of markers was ranked via the Mean DecreaseAccu racy measure and the average over the 1000 Random Forests was calculated (y-axis).
  • Makers were sorted after increasing rank (decreasing importance for the classification performance).
  • Figure 8 Ranking of selected makers for UCa, CDa and Ctrl. Using all 35 markers (x- axis) 1000 random forests were trained to distinguish UCa, CDa and Ctrl. For each random forest the importance of markers was ranked via the Mean DecreaseAccu racy measure and the average over the 1000 Random Forests was calculated (y-axis). Makers were sorted after increasing rank (decreasing importance for the classification performance).
  • Figure 9 Ranking of selected makers for IBD vs Ctrl. Using all 35 markers (x-axis) 1000 random forests were trained to distinguish IBD vs Ctrl. For each random forest the importance of markers was ranked via the Mean DecreaseAccu racy measure and the average over the 1000 Random Forests was calculated (y-axis). Makers were sorted after increasing rank (decreasing importance for the classification performance).
  • the present disclosure is based on the identification of genomic regions useful as markers of inflammatory bowel diseases (IBD), such as Crohn's disease (CD) or ulcerative colitis (UC). As shown in the examples, the inventors have established that these markers can be used not only to diagnose whether a subject suffers from an IBD, but can also be used to discriminate between CD and UC, based on expression signatures characteristic of each disorder. Definitions
  • IBD Inflammatory bowel diseases
  • UC ulcerative colitis
  • IBD ulcers and inflammation of the inner lining of the intestines lead to symptoms of abdominal pain, diarrhea, and rectal bleeding. Ulcerative colitis occurs in the large intestine, while in Crohn's, the disease can involve the entire Gl tract as well as the small and large intestines.
  • IBD is a chronic condition with symptoms lasting for months to years. It is most common in young adults, but can occur at any age. It is found worldwide, but is most common in industrialized countries such as the United States, England, and northern Europe.
  • IBD The clinical symptoms of IBD are intermittent rectal bleeding, cramping abdominal pain, weight loss and diarrhea. Diagnosis of IBD is based on the clinical symptoms, the use of a barium enema, but direct visualization (sigmoidoscopy or colonoscopy) is the most accurate test. Protracted IBD is a risk factor for colon cancer, and treatment of IBD can involve medications and surgery.
  • Crohn's disease The main difference between Crohn's disease and UC is the location and nature of the inflammatory changes. Crohn's can affect any part of the gastrointestinal tract, from mouth to anus (skip lesions), although a majority of the cases start in the terminal ileum. Ulcerative colitis, in contrast, is restricted to the colon and the rectum.
  • UC ulcerative colitis
  • prognosis for patients with disease limited to the rectum (proctitis) or UC limited to the end of the left colon (proctosigmoiditis) is better than that of full colon UC.
  • Brief periodic treatments using oral medications or enemas may be sufficient.
  • blood loss from the inflamed intestines can lead to anemia, and may require treatment with iron supplements or even blood transfusions.
  • the colon can acutely dilate to a large size when the inflammation becomes very severe. This condition is called toxic megacolon.
  • Patients with toxic megacolon are extremely ill with fever, abdominal pain and distention, dehydration, and malnutrition. Unless the patient improves rapidly with medication, surgery is usually necessary to prevent colon rupture.
  • IBD may be treated medicinally.
  • the most commonly used medications to treat IBD are anti-inflammatory drugs such as the salicylates.
  • the salicylate preparations have been effective in treating mild to moderate disease. They can also decrease the frequency of disease flares when the medications are taken on a prolonged basis.
  • Examples of salicylates include sulfasalazine, azulfidine, olsalazine, and mesalamine. All of these medications are given orally in high doses for maximal therapeutic benefit. These medicines are not without side effects.
  • Azulfidine can cause upset stomach when taken in high doses, and rare cases of mild kidney inflammation have been reported with some salicylate preparations.
  • Corticosteroids are more potent and faster-acting than salicylates in the treatment of IBD, but potentially serious side effects limit the use of corticosteroids to patients with more severe disease. Side effects of corticosteroids usually occur with long-term use. They include thinning of the bone and skin, increased susceptibility to infections, diabetes, hypertension, glaucoma, muscle wasting/weakness, rounding of the face, psychiatric disturbances, and, on rare occasions, destruction of hip joints.
  • immunosuppressants include azathioprine and 6-mercaptopurine. Immunosuppressants used in this situation help to control IBD and allow gradual reduction or elimination of corticosteroids. However, immunosuppressants render the patient immuno-compromised and susceptible to many other diseases.
  • IBD inflammatory bowel disease
  • ulcerative colitis or Crohn's disease is based on visual inspection of the gut through endoscopy, and histology assessment of pinch biopsies taken in the same colonoscopy, but can it also include radiology, x-ray and
  • Remission denotes herein periods with disease control versus active disease which are often referred to as "attack”. It generally refers to the state of absence of disease activity in patients known to have a chronic illness that cannot be cured. It is commonly used to refer to absence of active inflammatory bowel disease which is expected to manifest again in the future. A patient in remission thus exhibits no disease activity of IBD, UC or CD. Relapse
  • relapse denotes herein re-occurence of the symptoms of IBD.
  • the most common early symptoms of IBD are chronic diarrhea (which is sometimes bloody), cramping abdominal pain, fever, loss of appetite, and weight loss. Symptoms may continue for days or weeks and may resolve without treatment. IBD relapses at irregular intervals throughout the lifespan of a subject. Relapse can be mild or severe, brief or prolonged. Severe relapses can lead to intense pain, dehydration, and blood loss. Symptomatic periods may also be referred to as flares.
  • a patient in relapse is a patient with active IBD, UC or CD.
  • treatment refers to the management and care of a patient for the purpose of combating a condition, disease or disorder.
  • the term is intended to include the full spectrum of treatments for a given condition from which the patient is suffering, such as administration of the active compound for the purpose of: alleviating or relieving symptoms or complications; delaying the progression of the condition, disease or disorder; curing or eliminating the condition, disease or disorder; and/or preventing the condition, disease or disorder, wherein "preventing" or
  • prevention is to be understood to refer to the management and care of a patient for the purpose of hindering, reducing or delaying the development of the condition, disease or disorder, and includes the administration of the active compounds to prevent or reduce the risk of the onset of symptoms or complications.
  • the patient to be treated is preferably a mammal, in particular a human being.
  • the patients to be treated according to the present invention can be of various ages.
  • RNAs can, but does not have to correspond to annotated genes, and does not necessarily correspond to mRNAs.
  • An expression profile is a measurement of the expression levels of at least two markers. Markers may refer to know genes or un-annotated genes, including long non- coding RNAs and enhancer RNAs. In the present disclosure, the term preferably refers to RNA expression levels of at least two markers in a sample.
  • the sample is preferably derived from a subject for which no diagnosis of IBD, CD or UC is confirmed.
  • reference sample a sample derived from a subject for which a diagnosis of IBD, CD or UC has been established in other ways than using the present methods.
  • Sensitivity refers to the test's true positive rate - the proportion of positives (e.g. IBD patients) that are predicted as such.
  • a negative result in a method with high sensitivity is useful for ruling out the disease.
  • a high sensitivity test is reliable when its result is negative, since it rarely misdiagnoses those who have the disease.
  • a test with 100% sensitivity will recognize all patients with the disease.
  • a negative test result would definitively rule out presence of the disease in a patient.
  • a positive result in a test with high sensitivity is not useful for ascertaining that the subject has the disease.
  • Specificity relates to the true negative rate, i.e. it reflects the ability of a diagnostic method to correctly detect subjects without a condition.
  • the specificity of a test is the proportion of negative (e.g. non-IBD) subjects who were also predicted to be negative.
  • a positive result in a test with high specificity is useful for ascertaining that the subject has the disease. Such high specificity methods rarely yield positive results in healthy subjects.
  • a test with 100% specificity will read negative and accurately exclude disease for all healthy patients, while a positive result signifies a high probability of the presence of disease.
  • the accuracy of a diagnostic method refers to the amount of agreement between the results of a method under evaluation and the results of a reference standard or test. It is the proportion of true results (both true positives and true negatives) vs. the total number of cases examined.
  • the present methods are particularly useful for diagnosing whether a subject suspected of suffering from an IBD such as UC or CD is healthy or does suffer from an IBD.
  • the present methods can also be used to discriminate between subjects suffering from UC and subjects suffering from CD. This is important since treatments of UC and CD differ.
  • the subjects may have been diagnosed by methods otherwise known in the art, whereby the present methods are useful for confirming the diagnosis, or there may be no diagnosis yet, but a suspicion, e.g. based on known symptoms of IBD, that the subject suffers from IBD.
  • diagnosis of IBDs is based on visual inspection of the gut through endoscopy, and histology assessment of pinch biopsies taken in the same colonoscopy. Methods may also involve radiology analysis, X-ray analysis and microbiology-based methods. The pinch biopsy is usually from the descending colon.
  • the main goal of treatment of IBD, UC or CD is to induce remission. Once remission has been induced, the therapy is changed and the goal is to maintain remission.
  • the treatments employed to induce remission are usually different from the treatments used to maintain remission.
  • Conventional treatments for UC patients include administration of mesalamine at the first stage, which is effective for both induction and maintenance of remission in mild to moderate patients.
  • the next line of treatment is either conventional corticosteroids or multimatrix
  • budesonide also known as Uceris, Pulmicort or Rhinocort
  • Uceris Pulmicort or Rhinocort
  • vedolizumab is effective for induction and maintenance of remission of ulcerative colitis and is corticosteroid-sparing. Approximately 25%-35% of ulcerative colitis patients will ultimately require surgery - typically colectomy.
  • administration and regimens may also differ.
  • a review is provided in Wehkamp et al., Dtsch Cardioebl Int 2016; 1 13: 72-82, particularly in e Figurel and e Figure 2.
  • Markers useful for diagnosing an inflammatory bowel disease are markers useful for diagnosing an inflammatory bowel disease
  • the present disclosure relates to the identification of markers useful for determining whether a subject suffers from an inflammatory bowel disease.
  • the markers can also be used to discriminate whether the subject suffers from ulcerative colitis, from Crohn's disease or from another inflammatory bowel disease.
  • CAGE was performed on biopsies from the descending colon from IBD patients and controls, providing a genome-wide map of TSS (transcription start sites for known and unknown RNAs and genes) across individuals with and without IBD.
  • TSS transcription start sites for known and unknown RNAs and genes
  • the inventors identified sets of marker regions - genomic regions, whose RNA expression was useful in distinguishing controls, UC and CD samples.
  • markers do not necessarily correspond to coding genomic regions or known genes - they often correspond to un-annotated non-coding RNAs.
  • the expression of such markers can be obtained from samples of subjects suffering from or suspected of suffering from an IBD such as UC or CD. Expression signatures derived from these markers can then be compared to reference expression signatures derived above, which in turn allows for determining whether the subject indeed suffers from an IBD such as CD or UC.
  • Marker expression, and thereby expression profiles can be determined by methods known in the art such as quantitative PCR (qPCR) or hybridization based measurement methods such as microarray analysis.
  • qPCR quantitative PCR
  • hybridization based measurement methods such as microarray analysis.
  • useful primer sets which can be used to establish expression profiles in a sample.
  • the methods disclosed herein may comprise a step of extracting RNA from a sample prior to analysing the expression profiles.
  • the present methods are based on measuring expression profiles in a sample from a subject suffering from or suspected of suffering from an IBD, for example UC or CD.
  • the sample from which the expression profiles are measured may be a sample from the colon, preferably the descending colon of a subject.
  • the sample is a pinch biopsy, for example from the colon, preferably the descending colon.
  • the sample may be a sample from an inflamed segment of the descending colon.
  • markers which can be used to diagnose an IBD.
  • the markers can also be used to discriminate between UC and CD.
  • a method of diagnosing an inflammatory bowel disease comprising the steps of:
  • markers such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers in said sample, wherein the markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID
  • the genomic regions as set forth in SEQ ID NO: 71 to SEQ ID NO: 105 are regions which display an expression profile in subjects suffering from IBD which is different from their expression profile in healthy subjects. They correspond to transcription start sites (TSS) as identified by CAGE, as shown in the examples.
  • TSS transcription start sites
  • markers may be more useful for diagnosing a given state than another.
  • some markers may be more specific for diagnosing UC than for diagnosing CD; while others may help discriminate between IBD patients and healthy subjects.
  • the expression profiles of 2 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 3 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 4 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 5 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 6 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 7 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 8 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 9 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 10 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 1 1 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 12 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 13 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 14 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 15 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 16 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 17 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 18 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 19 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 20 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 21 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 22 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 23 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 24 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 25 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 26 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 27 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 28 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 29 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 30 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 31 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 32 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 33 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 34 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105.
  • the expression profiles of 35 markers are analysed, wherein the markers are selected from the group consisting of SEQ ID NO: 71 -105. It will be clear to the person of skill in the art that the whole region as set forth in any of SEQ ID NO: 71 -105 need not necessarily be amplified.
  • the at least 2 markers are thus selected from a group of genomic regions comprising at least part of a consecutive sequence comprised in each of SEQ ID: 71 -105.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as at least 25 markers, such as at least 26 markers, such as at least 27 markers, such as at least 28 markers, such as at least 29 markers, such as at least 30 markers, such as at least 31 markers, such
  • genomic regions selected as markers can vary somewhat. Said genomic regions are used as markers for determining an expression profile by hybridisation-based methods, as described herein.
  • the choice of the boundaries may vary and be dictated by the usual constraints of primer design, for example the sequence (to avoid formation of secondary structures potentially jeopardising the analysis, or the constraints linked to two primers in a pair having preferably similar melting temperatures), so that the expression profiles from the selected genomic regions can be properly established by conventional methods.
  • the markers for diagnosing if the subject suffers from an IBD such as UC or CD are selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 15, SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 1 18, SEQ ID NO: 1 19, SEQ ID NO: 120, SEQ ID NO: 121 , SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131 , SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO:
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101 , SEQ ID NO: 103 and SEQ ID NO: 105.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as at least 25 markers, such as at least 26 markers, such as 27 markers, selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO:
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers, selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101 , SEQ ID NO: 103 and SEQ ID NO: 105.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as at least 25 markers, such as at least 26 markers, such as 27 markers, selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO:
  • SEQ ID NO: 133 SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 138 and SEQ ID NO: 140.
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 15, SEQ ID NO: 1 16, SEQ ID NO
  • markers for determining if a subject is healthy or suffers from an IBD are the markers as set forth in SEQ ID NO: 76, SEQ ID NO: 82, SEQ ID NO: 94, SEQ ID NO: 99 and SEQ ID NO: 102.
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as 5 markers selected from the group consisting of SEQ ID NO: 76, SEQ ID NO: 82, SEQ ID NO: 94, SEQ ID NO: 99 and SEQ ID NO: 102.
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as 5 markers selected from the group consisting of SEQ ID NO: 1 1 1 , SEQ ID NO: 1 17, SEQ ID NO: 129, SEQ ID NO: 134 and SEQ ID NO: 137.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 94, SEQ ID NO: 88, SEQ ID NO: 103, SEQ ID NO: 76, SEQ ID NO: 84, SEQ ID NO: 99, SEQ ID NO: 81 , SEQ ID NO: 102, SEQ ID NO: 82, SEQ ID NO: 79, SEQ ID NO: 95, SEQ ID NO: 92, SEQ ID NO: 72, SEQ ID NO: 100, SEQ ID NO: 104, SEQ ID NO: 91 , SEQ ID NO: 105, SEQ ID NO: 75, SEQ ID NO: 97, SEQ ID NO: 71 , SEQ ID NO: 74, SEQ ID NO: 78, SEQ ID NO: 101 , SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 90, SEQ ID NO: 77
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 94, SEQ ID NO: 88, SEQ ID NO: 103, SEQ ID NO: 76, SEQ ID NO: 84, SEQ ID NO: 99, SEQ ID NO: 81 , SEQ ID NO: 102, SEQ ID NO: 82, SEQ ID NO: 79, SEQ ID NO
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as 10 markers selected from the group consisting of SEQ ID NO: 94, SEQ ID NO: 88, SEQ ID NO: 103, SEQ ID NO: 76, SEQ ID NO: 84, SEQ ID NO: 99, SEQ ID NO: 81 , SEQ ID NO: 102, SEQ ID NO: 82 and SEQ ID NO: 79.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 129, SEQ ID NO: 123, SEQ ID NO: 138, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 19, SEQ ID NO: 134, SEQ ID NO: 1 16, SEQ ID NO: 137, SEQ ID NO: 1 17, SEQ ID NO: 1 14, SEQ ID NO: 130, SEQ ID NO: 127, SEQ ID NO: 107, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 126, SEQ ID NO: 140, SEQ ID NO: 1 10, SEQ ID NO: 132, SEQ ID NO: 106, SEQ ID NO: 109, SEQ ID NO: 1 13, SEQ ID NO: 136, SEQ ID NO: 131 , SEQ ID NO: 133, SEQ ID NO: 125, SEQ ID NO: 1 12, SEQ ID NO: 124, SEQ ID NO: 108, SEQ ID NO: 1 18, SEQ ID NO:
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 129, SEQ ID NO: 123, SEQ ID NO: 138, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 19, SEQ ID NO: 134, SEQ ID NO: 1 16, SEQ ID NO: 137, SEQ ID NO: 1 17, SEQ ID NO: 1 14, SEQ ID NO NO:
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as 10 markers selected from the group consisting of SEQ ID NO: 129, SEQ ID NO: 123, SEQ ID NO: 138, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 19, SEQ ID NO: 134, SEQ ID NO: 1 16, SEQ ID NO: 137, SEQ ID NO: 1 17 and SEQ ID NO: 1 14.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 84, SEQ ID NO: 92, SEQ ID NO: 88, SEQ ID NO: 80, SEQ ID NO: 99, SEQ ID NO: 76, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 91 , SEQ ID NO: 79, SEQ ID NO: 102, SEQ ID NO: 95, SEQ ID NO: 72, SEQ ID NO: 104, SEQ ID NO: 75, SEQ ID NO: 86, SEQ ID NO: 77, SEQ ID NO: 83, SEQ ID NO: 105, SEQ ID NO: 96, SEQ ID NO: 90, SEQ ID NO: 97, SEQ ID NO: 71 , SEQ ID NO: 74, SEQ ID NO: 89, SEQ ID NO: 101 , SEQ ID NO: 73, SEQ ID NO:
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 84, SEQ ID NO: 92, SEQ ID NO: 88, SEQ ID NO: 80, SEQ ID NO: 99, SEQ ID NO: 76, SEQ ID NO: 81 , SEQ ID NO: 100
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as 9 markers selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 84, SEQ ID NO: 92, SEQ ID NO: 88, SEQ ID NO: 80, SEQ ID NO: 99 and SEQ ID NO: 76.
  • markers are useful for determining if a subject suffers from UC, from CD or is healthy.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 129, SEQ ID NO: 138, SEQ ID NO: 1 19, SEQ ID NO: 127, SEQ ID NO: 123, SEQ ID NO: 1 15, SEQ ID NO: 134, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 126, SEQ ID NO: 1 14, SEQ ID NO: 137, SEQ ID NO: 130, SEQ ID NO: 107, SEQ ID NO: 139, SEQ ID NO: 1 10, SEQ ID NO: 121 , SEQ ID NO: 1 12, SEQ ID NO: 1 18, SEQ ID NO: 140, SEQ ID NO: 131 , SEQ ID NO: 125, SEQ ID NO: 132, SEQ ID NO: 106, SEQ ID NO: 109, SEQ ID NO: 124, SEQ ID NO: 136, SEQ ID NO: 108, SEQ ID NO: 135, S
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as at least 25 markers, such as 26 markers selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 129, SEQ ID NO: 138, SEQ ID NO: 1 19, SEQ ID NO: 127, SEQ ID NO: 123, SEQ ID NO: 1 15, SEQ ID NO: 134, SEQ ID NO: 1 1 1 , SEQ ID NO: 13
  • the at least 2 markers are at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as 9 markers selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 129, SEQ ID NO: 138, SEQ ID NO: 1 19, SEQ ID NO: 127, SEQ ID NO: 123, SEQ ID NO: 1 15, SEQ ID NO: 134 and SEQ ID NO: 1 1 1 .
  • markers are useful for determining if a subject suffers from UC, from CD or is healthy.
  • the expression levels from the above at least 2 markers is determined by quantitative PCR, as is also known in the art.
  • Useful primer pairs for determining the expression profiles from the present markers are provided herein, in particular primer pairs useful for diagnosing an IBD.
  • the primer pair is selected from the group consisting of:
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as at least 25 primer pairs, such as at least 26 primer pairs, such as at least 27 primer pairs, such as at least 28 primer pairs, such as at least 29 primer pairs, such as at least 30 primer pairs, such as at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as at least 25 primer pairs, such as at least 26 primer pairs, such as 27 primer pairs, selected from the group consisting of SEQ ID NO: 1 and SEQ ID NO: 2; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 5 and SEQ ID NO: 1 and
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as 25 primer pairs selected from the group consisting of SEQ ID NO: 1 and SEQ ID NO: 2; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 5 and SEQ ID NO: 6; SEQ ID NO: 9 and SEQ ID NO: 10;
  • the at least 2 primer pairs may be selected from the group consisting of the following pairs: SEQ ID NO: 1 1 and SEQ ID NO: 12; SEQ ID NO: 23 and SEQ ID NO: 24; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 57 and SEQ ID NO: 58; and SEQ ID NO: 63 and SEQ ID NO: 64.
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as 5 primer pairs selected from the group consisting of SEQ ID NO: 1 1 and SEQ ID NO: 12; SEQ ID NO: 23 and SEQ ID NO: 24; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 57 and SEQ ID NO: 58; and SEQ ID NO: 63 and SEQ ID NO: 64.
  • the at least 2 primer pairs are selected from the group consisting of: SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 35 and SEQ ID NO: 36; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 1 1 and SEQ ID NO: 12; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 57 and SEQ ID NO: 58; SEQ ID NO: 21 and SEQ ID NO: 22; SEQ ID NO: 63 and SEQ ID NO: 64; SEQ ID NO: 23 and SEQ ID NO: 24; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 49 and SEQ ID NO: 50; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 67 and SEQ ID NO: 68; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 59
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as 25 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 35 and SEQ ID NO: 36; SEQ ID NO: 65 and SEQ ID NO: 66;
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as 10 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 35 and SEQ ID NO: 36; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 1 1 and SEQ ID NO: 12; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 57 and SEQ ID NO: 58; SEQ ID NO: 21 and SEQ ID NO: 22; SEQ ID NO: 63 and SEQ ID NO: 64; SEQ ID NO: 23 and SEQ ID NO: 24; SEQ ID NO: 17 and SEQ ID NO: 18.
  • the primer pairs may be selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 35 and SEQ ID NO: 36; SEQ ID NO: 19 and SEQ ID NO: 20;
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as 25 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 27 and SEQ
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as 9 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 35 and SEQ ID NO: 36; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 57 and SEQ ID NO: 58; SEQ ID NO: 1 1 and SEQ ID NO: 12.
  • primer pairs are used, such as at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as at least 25 primer pairs, such as at least 26 primer pairs, such as at least 27 primer pairs, such as at least 28 primer pairs, such
  • the markers disclosed herein are useful for diagnosing if a subject suffers from ulcerative colitis.
  • markers such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers in said sample, wherein the markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 ,
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 75, SEQ ID NO: 81 , SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 100 and SEQ ID NO: 104.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as 6 markers selected from the group consisting of SEQ ID NO: 75, SEQ ID NO: 81 , SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 100 and SEQ ID NO: 104..
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as 6 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 9 and SEQ ID NO: 10; SEQ ID NO: 21 and SEQ ID NO: 22; SEQ ID NO: 43 and SEQ ID NO: 44: SEQ ID NO: 45 and SEQ ID NO: 50; SEQ ID NO: 59 and SEQ ID NO: 60; and SEQ ID NO: 67 and SEQ ID NO: 68.
  • the primer pairs are at least 2 primer pairs selected from the group consisting of the following pairs: SEQ ID NO: 9 and SEQ ID NO: 10; SEQ ID NO: 21 and SEQ ID NO: 22; SEQ ID NO: 43 and SEQ ID NO: 44: SEQ ID NO: 45 and SEQ ID NO: 50; SEQ ID NO: 59 and SEQ ID NO: 60; and SEQ ID NO: 67 and SEQ ID NO: 68.
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as 6 primer pairs.
  • the markers disclosed herein are also useful for diagnosing if a subject suffers from Crohn's disease.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 101 and SEQ ID NO: 105.
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as 19 markers.
  • markers such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as 19 markers.
  • the at least 2 markers are at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as 19 markers selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 18, SEQ ID NO: 1 19, SEQ ID NO: 120, SEQ ID NO: 121 , SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 131 , SEQ ID NO:
  • the at least 2 primer pairs may be selected from the group consisting of the following pairs: SEQ ID NO: 1 and SEQ ID NO: 2; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 4 and SEQ ID NO: 6; SEQ ID NO: 7 and SEQ ID NO: 8; SEQ ID NO: 13 and SEQ ID NO: 14; SEQ ID NO: 15 and SEQ ID NO: 16; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 25 and SEQ ID NO: 26; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 29 and SEQ ID NO: 30; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 33 and SEQ ID NO: 34; SEQ ID NO: 37 and SEQ ID NO: 38; SEQ ID NO: 39 and SEQ ID NO: 40; SEQ ID NO: 51 and SEQ ID NO: 52; SEQ ID NO: 53 and SEQ ID NO: 54; SEQ ID NO: 15 and SEQ ID NO
  • the at least 2 primer pairs are at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as 19 primer pairs selected from SEQ ID NO: 1 and SEQ ID NO: 2; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 4 and SEQ ID NO: 6; SEQ ID NO: 7 and SEQ ID NO: 8; SEQ ID NO: 13 and SEQ ID NO: 14; SEQ ID NO: 15 and SEQ ID NO: 16; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 25 and SEQ ID NO: 1 and S
  • markers are useful for discriminating whether a subject suffering from an IBD suffers from UC or from CD. Useful markers
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO: 84, SEQ ID NO: 97, SEQ ID NO: 81 , SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 95, SEQ ID NO: 99, SEQ ID NO: 73, SEQ ID NO: 90, SEQ ID NO: 72, SEQ ID NO: 85, SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 71 , SEQ ID NO: 74, SEQ ID NO: 94, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 104, SEQ ID NO: 93,
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as at least 25 markers, such as at least 26 markers, such as at least 27 markers, such as at least 28 markers, such as at least 29 markers, such as at least 30 markers, such as at least 31 markers, such as at least 32 markers, such as at least 33 markers, such as at least 34 markers, such as 35 markers, selected from a group of genomic regions comprising at least part of a consecutive sequence comprise
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO: 84, SEQ ID NO: 97, SEQ ID NO: 81 , SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 95, SEQ ID NO: 99, SEQ ID NO: 73, SEQ ID NO: 90, SEQ ID NO: 72, SEQ ID NO: 85, SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 71 and SEQ ID NO: 74.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO:
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79 and SEQ ID NO: 83.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as 7 markers selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79 and SEQ ID NO: 83.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 1 15, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 121 , SEQ ID NO: 1 14, SEQ ID NO: 1 18, SEQ ID NO: 1 10, SEQ ID NO: 1 12, SEQ ID NO: 124, SEQ ID NO: 1 19, SEQ ID NO: 132, SEQ ID NO: 1 16, SEQ ID NO: 138, SEQ ID NO: 1 17, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 108, SEQ ID NO: 125, SEQ ID NO: 107, SEQ ID NO: 120, SEQ ID NO: 131 , SEQ ID NO: 137, SEQ ID NO: 106, SEQ ID NO: 109, SEQ ID NO: 129, SEQ ID NO: 122, SEQ ID NO: 123,
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 1 15, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 121 , SEQ ID NO: 1 14, SEQ ID NO: 1 18, SEQ ID NO: 1 10, SEQ ID NO: 1 12, SEQ ID NO: 124, SEQ ID NO: 1 19, S
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as at least 7 markers, such as at least 8 markers, such as at least 9 markers, such as at least 10 markers, such as at least 1 1 markers, such as at least 12 markers, such as at least 13 markers, such as at least 14 markers, such as at least 15 markers, such as at least 16 markers, such as at least 17 markers, such as at least 18 markers, such as at least 19 markers, such as at least 20 markers, such as at least 21 markers, such as at least 22 markers, such as at least 23 markers, such as at least 24 markers, such as 25 markers selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 1 15, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 121 , SEQ ID NO: 1 14, SEQ ID NO: 1 18, SEQ ID NO: 1 10, SEQ ID NO: 1 12, SEQ ID NO: 124, SEQ ID NO: 1 19, S
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 1 15, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 121 , SEQ ID NO: 1 14 and SEQ ID NO: 1 18.
  • the at least 2 markers may be at least 3 markers, such as at least 4 markers, such as at least 5 markers, such as at least 6 markers, such as 7 markers selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 1 15, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 121 , SEQ ID NO: 1 14 and SEQ ID NO: 1 18.
  • Useful primer pairs to discriminate whether a subject suffering from an IBD suffers from UC or CD are also provided herein.
  • the at least 2 primer pairs are selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 17 and SEQ ID NO: 18;
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as at least 25 primer pairs, such as at least 26 primer pairs, such as at least 27 primer pairs, such as at least 28 primer pairs, such as at least 29 primer pairs, such as at least 30 primer pairs, such as at least 31 primer pairs, such as at least 32 primer pairs, such as at least 33 primer pairs
  • the at least 2 primer pairs are selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 25 and SEQ ID NO: 26; SEQ ID NO: 9 and SEQ ID NO: 10; SEQ ID NO: 13 and SEQ ID NO: 14; SEQ ID NO: 37 and SEQ ID NO: 38; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 53 and SEQ ID NO: 54; SEQ ID NO: 21 and SEQ ID NO: 22; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 23 and SEQ ID NO: 24; SEQ ID NO: 49 and SEQ ID NO: 50; SEQ ID NO: 57 and
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as at least 7 primer pairs, such as at least 8 primer pairs, such as at least 9 primer pairs, such as at least 10 primer pairs, such as at least 1 1 primer pairs, such as at least 12 primer pairs, such as at least 13 primer pairs, such as at least 14 primer pairs, such as at least 15 primer pairs, such as at least 16 primer pairs, such as at least 17 primer pairs, such as at least 18 primer pairs, such as at least 19 primer pairs, such as at least 20 primer pairs, such as at least 21 primer pairs, such as at least 22 primer pairs, such as at least 23 primer pairs, such as at least 24 primer pairs, such as 25 primer pairs selected from the group consisting of SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ
  • the at least 2 primer pairs are selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 25 and SEQ ID NO: 26.
  • the at least 2 primer pairs may be at least 3 primer pairs, such as at least 4 primer pairs, such as at least 5 primer pairs, such as at least 6 primer pairs, such as 7 primer pairs selected from the group consisting of SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 19 and SEQ ID NO: 20; SEQ ID NO: 41 and SEQ ID NO: 42; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 25 and SEQ ID NO: 26. Marker combinations
  • At least two markers are SEQ ID NO: 102
  • at least one of the other markers is selected from SEQ ID NO: 96, SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 81 , SEQ ID NO: 95, SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: 86, SEQ ID NO: 71 , SEQ ID NO: 96, SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 81 , SEQ ID NO: 101 , SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: 86, SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 85, SEQ ID NO: 75 and SEQ ID NO: 76.
  • at least one of the other markers is selected from SEQ ID NO: 97, SEQ ID NO: 71 , SEQ ID NO: 98, SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 81 , SEQ ID NO: 95, SEQ ID NO: 83, SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73 and SEQ ID NO
  • At least one of the other markers is selected from SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 92, SEQ ID NO: 85, SEQ ID NO: 75, SEQ ID NO: 99, SEQ ID NO: 88 and SEQ ID NO: 79.
  • one of the at least two markers is SEQ ID NO: 100
  • at least one of the other markers is selected from SEQ ID NO: 97, SEQ ID NO: 81 , , SEQ ID NO: 95, SEQ ID NO: 101 , SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO:76 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78 and SEQ ID NO: 76.
  • At least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 95, SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 76 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88 and SEQ ID NO: 73.
  • At least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 81 , SEQ ID NO: 85 and SEQ ID NO: 89.
  • at least one of the other markers is selected from SEQ ID NO: 72 and SEQ ID NO: 89.
  • At least one of the other markers is selected from SEQ ID NO: 81 , SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77.
  • Preferably at least one of the other markers is selected from SEQ ID NO: 81 , SEQ ID NO: 99 and SEQ ID NO: 77.
  • At least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 105, SEQ ID NO: 81 , SEQ ID NO: 95, SEQ ID NO: 101 , SEQ ID NO: 83, SEQ ID NO: 103, SEQ ID NO: 85, SEQ ID NO: 99, SEQ ID NO: 88 and SEQ ID NO: 73.
  • Preferably at least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 95, SEQ ID NO: 83 and SEQ ID NO: 73.
  • At least one of the other markers is selected from SEQ ID NO: 131 , SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 130, SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12; preferably at least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO
  • At least one of the other markers is selected from SEQ ID NO: 121 , SEQ ID NO: 106, SEQ ID NO: 131 , SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12; preferably at least one of the other markers is selected from SEQ ID NO: 121 , SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 120; preferably at least one of the other markers is selected from SEQ ID NO: 121 , S
  • At least one of the other markers is selected from SEQ ID NO: 132, SEQ ID NO: 106, SEQ ID NO: 133, SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 130, SEQ ID NO: 1 18, SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108 and SEQ ID NO: 1 1 1 ; preferably at least one of the other markers is selected from SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 127, SEQ ID NO: 120, SEQ ID NO: 1 10, SEQ ID NO: 134, SEQ ID NO: 134, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID
  • At least one of the other markers is selected from SEQ ID NO: 132, SEQ ID NO: 1 16, SEQ ID NO: 130, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO:1 1 1 and SEQ ID NO: 1 12; preferably at least one of the other markers is selected from SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO:1 1 1 and SEQ ID NO
  • At least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 130, SEQ ID NO: 138, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12; preferably at least one of the other markers is selected from SEQ ID NO: SEQ ID NO: 138, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123 and SEQ ID NO: 108.
  • At least two markers is SEQ ID NO: 125, then at least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 1 16,
  • At least two markers is SEQ ID NO: 139
  • at least one of the other markers is selected from SEQ ID NO: 1 16, SEQ ID NO: 134,
  • At least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 130, SEQ ID NO: 1 18 and SEQ ID NO: 108.
  • the methods disclosed herein display surprisingly good sensitivity, specificity and accuracy thereby allowing for correct diagnosis and treatment of patients.
  • the specificity of a method for diagnosing a subject with UC is at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the sensitivity of such a method is at least 0.3. In preferred embodiments, the sensitivity is at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more. In some embodiments, the accuracy is at least 0.5. In preferred embodiments, the accuracy is at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more
  • the sensitivity of a method using at least 2 markers as disclosed herein for determining whether a subject suffers from CD is at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the specificity of a method using at least 2 markers as disclosed herein for determining whether a subject suffers from CD is at least 0.8 or more, such as 0.85 or more, such as 0.9 or more, such as 0.95 or more.
  • the accuracy of a method using at least 2 markers as disclosed herein for determining whether a subject suffers from CD is at least 0.7 or more, such as 0.75 or more, such as 0.8 or more, such as 0.85 or more, such as 0.9 or more, such as 0.95 or more.
  • the specificity of a method for determining whether a subject is healthy is at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the sensitivity of a method for determining whether a subject is healthy is at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the accuracy of a method for determining whether a subject is healthy is at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the present markers are useful in computer implemented methods for automatically determining whether a subject is healthy or suffers from an IBD. Such methods comprise the steps of: i) comparing the expression profiles of at least 2 markers in a sample obtained from said subject with a first expression signature representative of healthy subjects and with a second expression signature representative of subjects suffering from an inflammatory bowel disease, wherein the markers are as defined herein, and wherein the expression profile represents the expression levels of the at least 2 markers together in said subject, the first expression signature represents the average expression levels of the at least 2 markers together in a group of at least 20 healthy subjects, and the second expression signature represents the average expression levels of the at least 2 markers together in a group of subjects suffering from an inflammatory bowel disease;
  • the method determines that the subject is healthy
  • the skilled person will know how to compare an expression profile with an expression signature.
  • the comparison may be done by a trained person, which can visually assess whether the overall shape of the expression profile from a given sample most resembles a first expression signature or a second expression signature, i.e. the trained person determines to which expression signature the expression profile is closest.
  • the trained person Upon assessment, the trained person then determines whether the subject is healthy or suffers from an IBD.
  • the comparison may also be done by a software.
  • Methods to train software to perform such classification of samples are known in the art, and may involve a machine learning algorithm such as Random Forests, Support Vector Machines, or neural networks.
  • a machine learning algorithm such as Random Forests, Support Vector Machines, or neural networks.
  • the algorithm can be trained to compare expression profiles from samples derived from subjects where no diagnosis has been precisely established with expression signatures characteristic of a disorder, and thereby predict whether the subject suffers from a given condition or is healthy.
  • Also disclosed herein is a method of diagnosing and treating an inflammatory bowel disease in a subject in need thereof, said method comprising the steps of:
  • a method of treating an inflammatory bowel disease wherein the disease is diagnosed as described herein above, before the subject suffering from the disease is treated.
  • the inflammatory bowel disease may be UC or CD.
  • the treatment may comprise or consist of mesalamine administration, corticosteroid administration, multimatrix administration, budesonide administration, infliximab administration, adalimumab administration, golimumab administration, vedolizumab administration, surgery, or of a combination thereof.
  • the choice of the therapeutic agent to be administered depends for example on the stage of the disease.
  • Mesalamine can be used in a first stage to induce remission and/or maintain remission in cases with mild or moderate exacerbation, while infliximab will be administered typically if remission cannot be established or maintained.
  • the treatment may comprise or consist of budesonide or sulfasalazine administration, corticosteroid administration, anti-tumor necrosis factor drug administration, such as infliximab, adalimumab and certolizumab pegol, surgery, or a combination thereof.
  • Sulfasalzine and budesonide are typically administered to subjects having mild to moderate exacerbation, while methotrexate may be appropriate for cases of recurrence or intolerance.
  • methotrexate may be appropriate for cases of recurrence or intolerance.
  • kits of parts comprising primers, instructions for use, optionally additional reagents for extracting RNA from biopsy samples, and optionally a software for diagnosing an inflammatory bowel disease, Crohn's disease or ulcerative colitis.
  • the primers are designed to allow measurement of an expression profile as disclosed herein from a sample derived from a subject suspected of suffering from an IBD, UC or CD.
  • the primers thus preferably allow the detection of at least two of the markers disclosed herein.
  • the kit thus preferably comprises at least two primer pairs, as described in the subsections "useful primers" above.
  • the present methods are based on the identification of a number of genomic regions which can be used as markers for an inflammatory bowel disease, ulcerative colitis and/or Crohn's disease. Starting from samples derived from subjects which are known to be healthy, or to suffer from an inflammatory bowel disease, such as ulcerative colitis or Crohn's disease, it is possible to identify genomic regions which display an expression profile which is characteristic for a given state (healthy, suffering from an IBD, suffering from UC or suffering from CD). Expression profiles which are
  • characteristic for samples derived from subjects suffering from one of the above diseases define expression signatures, which can then be used as reference in the methods of diagnosis disclosed herein.
  • the expression profiles of the same markers in samples derived from subjects suspected of suffering from a disease can be directly compared with the reference expression signatures, and a diagnosis can be made.
  • transcripts together representing a first transcriptome (ii) providing a second sample from a subject suffering from Crohn's disease, having a second set of transcripts together representing a second transcriptome;
  • transcripts at least part of the second set of transcripts and at least part of the third set of transcripts;
  • measuring and comparing the transcript levels can be performed at the genome-wide level by using transcriptome measurement methods such as RNA sequencing or 5'-RNA sequencing of capped RNAs (CAGE).
  • transcriptome measurement methods such as RNA sequencing or 5'-RNA sequencing of capped RNAs (CAGE).
  • the number of samples should be large enough.
  • the markers are identified using samples from at least 20 subjects in each of the groups to be compared (healthy, suffering from an IBD, suffering from UC, suffering from CD). While using larger numbers of samples may refine the accuracy, sensitivity and/or specificity of the method, this should be balanced with considerations on whether it is practically feasible to obtain and/or to analyse very large numbers of samples. Examples
  • Genome-wide 5'-RNA sequencing of capped RNAs can detect transcription start sites (TSSs) for known genes and un-annotated RNAs, such as non-cording RNAs.
  • TSSs transcription start sites
  • TSSs up-regulated in CDa vs. UCa defined as CD spec
  • TSSs up-regulated in UCa vs. CDa defined as UC spec
  • the number of TSSs within IBD up (4376) and IBD down (2536) was much larger than in CD spec (337) and UC spec (71 ) (Fig.2).
  • the inclusion of additional patient data in the analysis, i.e. gender and previous medication, did not affect the number of differentially expressed TSSs substantially, strongly suggesting these effects are minor compared to the CD/UC/Ctrl diagnosis.
  • Example 2 materials and methods
  • Cohort 1 was used for Cap Analysis of Gene Expression (CAGE) assay and subsequent microfluidics real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) validation.
  • This cohort included 25 patients with active UC (UCa), 17 patients with UC in remission (UCi), 20 patients with active CD (CDa), 3 patients with CD in remission (CDi) and 29 healthy controls (Ctrl).
  • the cohort included 37 UCa, 18 CDa, and 46 Ctrl subjects.
  • RNA from pinch biopsies from the descending colon cohort 1 (Fig.1 ).
  • biopsies were taken from inflamed segments, as confirmed by subsequent histology. All mucosal pinch biopsies, each approximately 15 mg, were obtained from the areas of the descending colon using routine endoscopic forceps. The descending colon was chosen to avoid any intersegmental variation.
  • the endoscopic diagnosis of active or inactive disease was confirmed by histopathology conducted on parallel biopsies taken within an inch of the 1 st biopsy.
  • the biopsies were immediately placed in RNAIater® Stabilization Solution (AmbionTM, Life Technologies) and kept at 4 ⁇ C for 24 hours before long term storage at -80 'C.
  • RNA integrity was determined using the 2100 Bioanalyzer Instrument (Agilent Technologies) with the Agilent RNA 6000 Pico Kit (Agilent Technologies) as recommended by manufacturer. In cohort 1 the average RNA integrity number (RIN) was 7.6 and no samples were below 5.3. For cohort 2 the average RIN value was 8.0 and no samples were below 6.2.
  • CAGE library preparation sequencing, mapping and processing.
  • CAGE libraries were prepared with an input of 1500 ng of total RNA as starting material.
  • CAGE libraries were prepared individually, but prior to sequencing four CAGE libraries with different barcodes were pooled and applied to the same sequencing lane. The following four barcodes were used: no.2 (CTT), no.3 (GAT), no.6 (ACG) and no.8 (ATC). All used primers and adaptors were purchased from Integrated DNA
  • TCs having ⁇ 1 TPM in at least 3 libraries were retained for further analysis.
  • CAGE-defined TSSs A summit, or 'TC peak', was identified in each TC, defined as the single base pair position within the TC with highest total TPM coverage across all samples.
  • CAGE-defined TSSs were annotated using Gencode v19 annotation (Harrow et al., 2012).
  • the canonical start site was defined as the most upstream annotated start site in the gene model.
  • CAGE-defined TSSs within ⁇ 100 bp of the most upstream annotated TSS for a Gencode-annotated gene were thus labelled as canonical TSSs.
  • CAGE-defined TSSs within ⁇ 100bp from all other annotated TSS were annotated as known alternative TSS.
  • CAGE-defined TSSs within gene bodies but >100bp from an annotated TSS were defined as novel alternative TSSs
  • CAGE-defined TSSs > 100 bp distant from gene annotation were annotated as novel intergenic TSSs
  • all TSSs located on the antisense strand to annotated genes were defined as novel antisense TSSs .
  • Some analyses were performed at the level of annotated genes, rather than on CAGE- defined TSS level. For these analyses, based on the annotation described above, we summed up all CAGE-defined TSSs overlapping the gene on the same strand. Statistical tests for differential expression of TSSs and genes.
  • the edgeR package (Robinson et al., 2009; McCarthy et al., 2012) was used to test for differential expression at both TSS- and gene-level using the GLM quasi-likelihood framework (default settings were used, with the exception that robust estimation at the empirical Bayes stage was used). Only CDa, UCa and Ctrl samples were included in this analysis. The four major batches were included as blocking factors. The following contrasts were used: i) IBD: average of CDa and UCa different from Ctrl and ii) CDvsUC: CD different from UC. Resulting P-values were corrected for multiple testing Benjamini-Hochberg method (producing FDR values).
  • TSSs or genes
  • the IBD up /IBD down sets corresponds to TSSs (or genes) with a positive/negative log2 fold change in contrast i)
  • the CDspec/UCspec sets corresponds to TSSs (or genes) with a positive/negative log2 fold change in contrast ii), where a positive log2 fold change corresponds to higher expression in CDa compared to UCa.
  • TSS regions As our main goal was classification by machine learning, we will refer to these TSS regions as "features" in this section. Because the shared inflammatory response in UCa and CDa vs. Ctrl was strong, we divided our analysis into an IBD set of features (shared CDa and UCa up- or down-regulation vs. Ctrl), and a set of features
  • edgeR14 edgeR14.
  • standard edgeR (fitGLM and glmLRT) was used to test for effects of CDa vs. Ctrl, UCa vs. Ctrl, CDa vs. UCa and CDa&UCa vs. Ctrl (shared inflammatory response), while controlling for batch effects.
  • Extracted TSSs had a Benjamini- Hochberg FDR ⁇ 0.05 and a
  • PLSDA Partial Least Squares Discriminant Analysis
  • a RF was trained to classify the patient labels based only on the data in that particular subset.
  • lowest Mean DecreaseAccu racy values lowest Mean DecreaseAccu racy values
  • Each RF was made with default parameters except specifying that 501 trees per forest should be generated and specifying the number of variables randomly sampled as candidates at each split by setting the 'mtry' parameter to (sqrt( x ) -1 ) * 2, where x was the number of features supplied to the individual RF.
  • the width of the TC was in the range of 2-100 nucleotides (both included), iii) the TC was expressed more than 10 TPM in at least 3 patients.
  • the ensemble produced 10 candidate sets for separating CDa & UCa from Ctrl (3 edgeR, 4 ComBat, 2 RandomForest, 1 PLSDA) and 5 candidate sets for separating CDa and UCa (edgeR, limma, 2 RandomForests, and PCA).
  • the two lists were merged and a short list of expert-cu rated known and novel biomarkers (21 TSSs and 10 enhancers) were added.
  • the combined list was then further pruned by manual curation, taking into account overall expression strength and genomic loci complexity.
  • the initial list comprised of 263 features, which was used for initial classification using CAGE data (see below).
  • Primers were designed using Primer3 (v.0.4.0)24 aiming for an amplicon length of 70 - 1 10 bp and a primer melting temperature of 60 'C calculated by the Breslauer thermodynamics (Breslauer et al., 1986). Primers were designed to be intron-spanning when possible, and each designed primer-set was analyzed with UCSC browser in- silico PCR tool in order to ensure a unique region would be amplified. Primers were synthesized by Integrated DNA Technologies (IDT).
  • IDTT Integrated DNA Technologies
  • Primer amplification efficiencies and dynamic ranges were acquired from standard curves constructed from several separate dilution series of pooled cDNA: with the dilutions 1 :5, 1 :25, 1 :100, 1 :500 and 1 :2500.
  • melting curves of amplicons were measured to certify primer specificity. 161 primer pairs (features) successfully passed our quality control and were used for analysis of cohort 1 on the Fluidigm ® platform.
  • RNA synthesis was performed using the QuantiTECT Reverse Transcription kit (Qiagen), containing a mix of random primers and oligo-dT, according to the manufacturer's instructions. Two separate cDNA reactions were performed for each RNA sample. Preamplification was performed using TaqMan PreAmp Master Mix (Applied Biosystems).
  • a 500 ⁇ primer mix (200 nM) combining all primers to be used on the Fluidigm® plate was prepared by pooling 5 ⁇ of all primerpairs (20 ⁇ ) and filling up the remaining volume with low EDTA TE-buffer (VWR International).
  • TaqMan PreAmp Master Mix (5 ⁇ ) was mixed with 2.5 ⁇ of the 200 nM primer mix, 2.5 ⁇ diluted cDNA, and incubated at 95 °C for 10 min, followed by 15 to 21 cycles of 95 °C for 15 s and 60 'C for 4 min (the number of cycles depended on the expression measured by CAGE).
  • Exonuclease I 16 U was added to the preamplified cDNA, and incubated 30 min at 37 ⁇ C, 80 °C for 15 min.
  • the preamplified cDNA was diluted with low EDTA TE-buffer (VWR International) either 1 :5 if the cDNA was preamplified for 21 cycles or 1 :10 if the cDNA was preamplified for 19 or 15 cycles.
  • RNA expression was analyzed by real-time qRT-PCR in the microfluidics system BioMarkTM 96.96 Dynamic Array (Fluidigm ® ).
  • the following cycle parameter was used: Thermal Mix with 2 min at 50 ⁇ C, 30 min at 70 ⁇ C, 10 min at 25 ⁇ C, UNG and Hot start with 2 min at 50 ⁇ C, 10 min at 95 ⁇ C, followed by 35 cycles with denaturing for 15 s at 95 °C and annealing/elongation for 1 min at 60 °C. Melting curves were generated after each run to confirm a single PCR product (from 60 'C to 95 'C, increasing 1 ⁇ C/3 s). Reactions were performed in duplicates (cDNA replicates).
  • Non-template controls (NTC) were included to indicate potential problems with non-specific amplification or sample contaminations.
  • Non-reverse transcriptase controls were included to assess potential DNA contamination.
  • the 161 features were reduced to 36 features by ranking the features for classification power.
  • a RF was trained to predict subject groups, both using all groups and one-vs-rest specification (i.e. UCa vs. non-UCa) using the randomForest R package (Skovgaard et al., 2013).
  • the optimal value for the mtry parameter was found using 100 five-fold cross-validations using the caret package
  • cDNA synthesis and preamplification was performed as described above for cohort 1 with an adjustment of the number of pre-amplification cycles. In this cohort cDNA was either preamplified 15 or 20 cycles, depending on expression level of the primer targets. The preamplified cDNA was diluted with low EDTA TE-buffer (VWR
  • RNA expression was analyzed by real-time qRT-PCR in the microfluidics system BioMarkTM 192.24 Dynamic Array (Fluidigm ® ) following the same protocol as used for the cohort 1 runs, with volumes adjusted to the 192.24 format, as described by manufacturer. Expression data (ACq values) were acquired and treated similar to cohort 1 (see above).
  • the first step was a RF trained to distinguish IBD (CDa and UCa) from healthy subjects (Ctrl) and the second step was a RF trained to distinguish CDa from UCa.
  • the two-step approach was chosen over an all-in-one approach because it was based on 5-fold cross- validation in the CAGE data resulting in better CDa sensitivities (data not shown).
  • m indicating the number of variables randomly sampled as candidates at each split
  • n indicating the minimum size of terminal nodes (corresponding to the mtry and nodesize options in the R
  • m and n parameters were chosen as the combination giving the highest overall accuracy in the two-step RF approach based on the average result of 5-fold cross-validation in cohort 1 . Apart from this all RFs were created with default parameters except specifying that each RF should have 1001 trees.
  • To assess the accuracy of the classification model we performed 101 RF iterations of 5-fold cross validation.
  • Reverse primers SEQ ID NO: 60, SEQ ID NO: 48, SEQ ID NO: 66.
  • Reverse primers SEQ ID NO: 60, SEQ ID NO: 20, SEQ ID NO: 42, SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 36.
  • Reverse primers SEQ ID NO: 60, SEQ ID NO: 20, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 32, SEQ ID NO: 48, SEQ ID NO: 66, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 12.
  • EBSeq an empirical Bayes hierarchical model for inference in RNA-seq experiments. Nat genet 29, 1035-1043 (2013).
  • SEQ ID NO 20 SLC9A3R2 CTCCACAGCCTTGATCCTTT
  • SEQ ID NO: 70 NA CCATTTGTCTCCGGGTAAGA
  • ALKBH4 SEQ ID NO: 83 SEQ ID NO 1 18
  • HSD3B2 SEQ ID NO: 86 SEQ ID NO 121
  • CDX2 SEQ ID NO: 91 SEQ ID NO 126
  • GABARAPL2 SEQ ID NO: 93 SEQ ID NO 128
  • WFDC2 SEQ ID NO: 96 SEQ ID NO 131
  • HNF4G SEQ ID NO: 100 SEQ ID NO 135
  • HMGCS2 SEQ ID NO: 103 SEQ ID NO 138
  • a method of diagnosing an inflammatory bowel disease comprising the steps of a. providing a sample from a subject suffering from or suspected of suffering from an inflammatory bowel disease such as ulcerative colitis or Crohn's disease;
  • markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91 , SEQ ID NO:
  • markers are selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 15, SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 1 18, SEQ ID NO: 1 19, SEQ ID NO: 120, SEQ ID NO: 121 , SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131 , SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 106, SEQ ID NO:
  • the method of diagnosis can discriminate between healthy subjects and subjects suffering from an inflammatory bowel disease.
  • the method according to any one of the preceding items, wherein the method of diagnosis can discriminate between subjects suffering from Crohn's disease and subjects suffering from ulcerative colitis.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101 , SEQ ID NO: 103 and SEQ ID NO: 105.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 15, SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 1 18, SEQ ID NO: 120, SEQ ID NO: 121 , SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 131 , SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 138 and SEQ ID NO: 140.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 71 , SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101 , SEQ ID NO: 103 and SEQ ID NO: 105.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 12, SEQ ID NO: 1 13, SEQ ID NO: 1 14, SEQ ID NO: 1 15, SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 1 18, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 131 , SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 138 and SEQ ID NO: 140.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 76, SEQ ID NO: 82, SEQ ID NO: 94, SEQ ID NO: 99 and SEQ ID NO: 102.
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 84, SEQ ID NO: 92, SEQ ID NO: 88, SEQ ID NO: 80, SEQ ID NO: 99, SEQ ID NO: 76, SEQ ID NO: 81 , SEQ ID NO:
  • SEQ ID NO: 91 SEQ ID NO: 79, SEQ ID NO: 102, SEQ ID NO: 95, SEQ ID NO: 72, SEQ ID NO: 104, SEQ ID NO: 75, SEQ ID NO: 86, SEQ ID NO: 77, SEQ ID NO: 83, SEQ ID NO: 105, SEQ ID NO: 96, SEQ ID NO: 90, SEQ ID NO: 97, SEQ ID NO: 71 , SEQ ID NO: 74, SEQ ID NO: 89, SEQ ID NO: 101 , SEQ ID NO: 73, SEQ ID NO: 98, SEQ ID NO: 87, SEQ ID NO: 93, SEQ ID NO: 85 and SEQ ID NO: 78, preferably the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 84, SEQ ID NO: 92, SEQ ID NO: 88, SEQ ID NO:
  • SEQ ID NO: 1 SEQ ID NO: 1 15, SEQ ID NO: 134, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 126, SEQ ID NO: 1 14, SEQ ID NO: 137, SEQ ID NO: 130, SEQ ID NO: 107, SEQ ID NO: 139, SEQ ID NO: 1 10, SEQ ID NO:
  • SEQ ID NO: 1 12 SEQ ID NO: 1 18, SEQ ID NO: 140, SEQ ID NO: 131 , SEQ ID NO: 125, SEQ ID NO: 132, SEQ ID NO: 106, SEQ ID NO: 109, SEQ ID NO: 124, SEQ ID NO: 136, SEQ ID NO: 108, SEQ ID NO: 133, SEQ ID NO:
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 135, SEQ ID NO: 129, SEQ ID NO: 138, SEQ ID NO: 1 19, SEQ ID NO: 127, SEQ ID NO: 123, SEQ ID NO: 1 15, SEQ ID NO: 134, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 16, SEQ ID NO: 1 17, SEQ ID NO: 126, SEQ ID NO: 1 14, SEQ ID NO: 137,
  • SEQ ID NO: 81 SEQ ID NO: 102, SEQ ID NO: 82, SEQ ID NO: 79, SEQ ID NO: 95, SEQ ID NO: 92, SEQ ID NO: 72, SEQ ID NO: 100, SEQ ID NO: 104, SEQ ID NO: 91 , SEQ ID NO: 105, SEQ ID NO: 75, SEQ ID NO: 97, SEQ ID NO: 71 , SEQ ID NO: 74, SEQ ID NO: 78, SEQ ID NO: 101 , SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 90, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO: 73,
  • SEQ ID NO: 83, SEQ ID NO: 87, SEQ ID NO: 86, SEQ ID NO: 93, SEQ ID NO: 80 and SEQ ID NO: 85 preferably the at least 2 markers are selected from the group consisting of SEQ ID NO: 94, SEQ ID NO: 88, SEQ ID NO: 103, SEQ ID NO: 76, SEQ ID NO: 84, SEQ ID NO: 99, SEQ ID NO: 81 , SEQ ID NO: 102, SEQ ID NO: 82, SEQ ID NO: 79, SEQ ID NO: 95, SEQ ID NO: 92, SEQ ID NO:
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 94, SEQ ID NO: 88, SEQ ID NO: 103, SEQ ID NO: 76, SEQ ID NO: 84, SEQ ID NO: 99,
  • SEQ ID NO: 81 SEQ ID NO: 102, SEQ ID NO: 82 and SEQ ID NO: 79.
  • SEQ ID NO: 128, SEQ ID NO: 1 15 and SEQ ID NO: 120 preferably the at least 2 markers are selected from the group consisting of SEQ ID NO: 129, SEQ ID NO: 123, SEQ ID NO: 138, SEQ ID NO: 1 1 1 , SEQ ID NO: 1 19, SEQ ID NO: 134, SEQ ID NO: 1 16, SEQ ID NO: 137, SEQ ID NO: 1 17, SEQ ID NO: 1 14, SEQ ID NO: 130, SEQ ID NO: 127, SEQ ID NO: 107, SEQ ID NO: 135,
  • SEQ ID NO: 80 SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO: 84, SEQ ID NO: 97, SEQ ID NO: 81 , SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 95, SEQ ID NO: 99, SEQ ID NO: 73, SEQ ID NO: 90, SEQ ID NO: 72, SEQ ID NO: 85, SEQ ID NO: 96, SEQ ID NO: 102, SEQ ID NO: 71 , SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 89, SEQ ID NO
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO: 79, SEQ ID NO: 83, SEQ ID NO:
  • the at least 2 markers are selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 80, SEQ ID NO: 91 , SEQ ID NO: 92, SEQ ID NO: 86, SEQ ID NO:
  • SEQ ID NO: 34 SEQ ID NO: 37 and SEQ ID NO: 38; SEQ ID NO: 39 and SEQ ID NO: 40; SEQ ID NO: 51 and SEQ ID NO: 52; SEQ ID NO: 53 and SEQ ID NO: 54; SEQ ID NO: 55 and SEQ ID NO: 56; SEQ ID NO: 61 and SEQ ID NO: 62; and SEQ ID NO: 69 and SEQ ID NO: 70.
  • SEQ ID NO: 67 and SEQ ID NO: 68 The method according to any one of the preceding items, wherein the expression profile is analysed by qPCR performed with a primer pair selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 68.
  • SEQ ID NO: 42 SEQ ID NO: 17 and SEQ ID NO: 18; SEQ ID NO: 63 and SEQ ID NO: 64; SEQ ID NO: 49 and SEQ ID NO: 50; SEQ ID NO: 3 and SEQ ID NO: 4; SEQ ID NO: 67 and SEQ ID NO: 68; SEQ ID NO: 9 and SEQ ID NO: 10; SEQ ID NO: 31 and SEQ ID NO: 32; SEQ ID NO: 13 and SEQ ID NO: 14; SEQ ID NO: 25 and SEQ ID NO: 26; SEQ ID NO: 69 and SEQ ID NO: 70; SEQ ID NO: 51 and SEQ ID NO: 52; SEQ ID NO: 39 and SEQ ID NO: 40; SEQ
  • the primer pair is selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 47 and SEQ ID NO: 48; SEQ ID NO: 65 and SEQ ID NO: 66; SEQ ID NO: 27 and SEQ ID NO: 28; SEQ ID NO: 43 and SEQ ID NO: 44; SEQ ID NO: 35 and SEQ ID NO:
  • the primer pair is selected from the group consisting of the following pairs: SEQ ID NO: 59 and SEQ ID NO: 60; SEQ ID NO: 47 and SEQ ID NO: 48;
  • sample is a sample from the colon, preferably the descending colon of said subject.
  • sample is a pinch biopsy, for example a sample from the colon, preferably the descending colon.
  • At least two markers is SEQ ID NO: 102, then at least one of the other markers is selected from SEQ ID NO: 96, SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 81 , SEQ ID NO: 95, SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 80, SEQ ID NO: 75,
  • SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77 preferably at least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77; or
  • At least two markers is SEQ ID NO: 94, then at least one of the other markers is selected from SEQ ID NO: 86, SEQ ID NO: 71 , SEQ ID NO: 96, SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 87, SEQ ID NO: 81 , SEQ ID NO: 101 , SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO:
  • SEQ ID NO: 88 SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO: 76 and SEQ ID NO: 77, preferably at least one of the other markers is selected from SEQ ID NO: 86, SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 85, SEQ ID NO: 75 and SEQ ID NO: 76; or
  • SEQ ID NO: 101 SEQ ID NO: 103, SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88, SEQ ID NO: 79, SEQ ID NO: 73, SEQ ID NO: 78, SEQ ID NO:76 and SEQ ID NO: 77, preferably at least one of the other markers is selected from SEQ ID NO: 92, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO:
  • At least two markers is SEQ ID NO: 84, then at least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 93, SEQ ID NO: 105, SEQ ID NO: 95, SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 85, SEQ
  • At least one of the other markers is selected from SEQ ID NO: SEQ ID NO: 103, SEQ ID NO: 82, SEQ ID NO: 85, SEQ ID NO: 80, SEQ ID NO: 75, SEQ ID NO: 89, SEQ ID NO: 99, SEQ ID NO: 88 and SEQ ID NO: 73; or (f) if one of the at least two markers is SEQ ID NO: 90, then at least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 81 , SEQ ID NO: 85 and SEQ ID NO: 89, preferably at least one of the other markers is selected from SEQ ID NO: 72 and SEQ ID NO: 89; or
  • SEQ ID NO: 78 SEQ ID NO: 76 and SEQ ID NO: 77, preferably at least one of the other markers is selected from SEQ ID NO: 81 , SEQ ID NO: 99 and SEQ ID NO: 77; or
  • SEQ ID NO: 95 SEQ ID NO: 101 , SEQ ID NO: 83, SEQ ID NO: 103, SEQ ID NO: 85, SEQ ID NO: 99, SEQ ID NO: 88 and SEQ ID NO: 73, preferably at least one of the other markers is selected from SEQ ID NO: 72, SEQ ID NO: 95, SEQ ID NO: 83 and SEQ ID NO: 73.
  • At least two markers is SEQ ID NO: 137, then at least one of the other markers is selected from SEQ ID NO: 131 , SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 130, SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 1 15, SEQ ID NO:
  • SEQ ID NO: 1 10 SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12, preferably at least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID
  • At least two markers is SEQ ID NO: 129, then at least one of the other markers is selected from SEQ ID NO: 121 , SEQ ID NO: 106, SEQ ID NO: 131 , SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO:
  • SEQ ID NO: 1 17 SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12, preferably at least one of the other markers is selected from SEQ ID NO: 121 , SEQ ID NO: 138, SEQ ID NO: 127, SEQ ID NO: 120, SEQ ID NO: 1 10 and SEQ ID NO: 1 1 1 ; or (c) if one of the at least two markers is SEQ ID NO: 126, then at least one of the other markers is selected from SEQ ID NO: 132, SEQ ID NO: 106, SEQ ID NO: 133, SEQ ID NO: 107, SEQ ID NO: 128, SEQ ID NO: 140, SEQ ID NO: 122, SEQ ID NO: 1 16, SEQ ID NO: 130, S
  • SEQ ID NO: 130 SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13, SEQ ID NO:1 1 1 and SEQ ID NO: 1 12, preferably at least one of the other markers is selected from SEQ ID NO: 127, SEQ ID NO: 1 17, SEQ ID NO: 120,
  • SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 13 and SEQ ID NO: 1 1 1 ; or
  • SEQ ID NO: 130 SEQ ID NO: 138, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO: 1 10, SEQ ID NO: 124, SEQ ID NO: 134, SEQ ID NO: 123, SEQ ID NO: 1 14, SEQ ID NO: 108, SEQ ID NO: 1 1 1 and SEQ ID NO: 1 12, preferably at least one of the other markers is selected from SEQ ID NO: SEQ ID NO: 138, SEQ ID NO: 1 17, SEQ ID NO: 120, SEQ ID NO: 1 15, SEQ ID NO:
  • At least one of the other markers is selected from SEQ ID NO: 107, SEQ ID NO: 140, SEQ ID NO: 1 17, SEQ ID NO: 130, SEQ ID NO: 136, SEQ ID NO: 1 18, SEQ ID NO: 138, SEQ ID NO: 120, SEQ ID NO: 134, SEQ ID NO: 123 and SEQ ID NO: 108, preferably at least one of the other markers is selected from SEQ ID NO: 107,
  • SEQ ID NO: 130 SEQ ID NO: 1 18 and SEQ ID NO: 108.
  • the sensitivity of the method for determining whether the subject suffers from UC is at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more. 43.
  • the specificity of the method for determining whether the subject suffers from UC is at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the accuracy of the method for determining whether the subject suffers from UC is at least 0.25, such as at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the sensitivity of the method for determining whether the subject suffers from CD is at least 0.05, such as at least 0.1 , such as at least 0.15, such as at least 0.2, such as at least 0.25, such as at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the specificity of the method for determining whether the subject suffers from CD is at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the accuracy of the method for determining whether the subject suffers from CD is at least 0.25, such as at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the sensitivity of the method for determining whether the subject is healthy is at least 00.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the specificity of the method for determining whether the subject is healthy is at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • the accuracy of the method for determining whether the subject is healthy is at least 0.25, such as at least 0.3, such as at least 0.35, such as at least 0.4, such as at least 0.45, such as at least 0.5, such as at least 0.55, such as at least 0.6, such as at least 0.65, such as at least 0.7, such as at least 0.75, such as at least 0.8, such as at least 0.85, such as at least 0.9, such as at least 0.95 or more.
  • a method of diagnosing and treating a disorder selected from ulcerative colitis or Crohn's disease in a subject suffering or suspected of suffering therefrom comprising the steps of:
  • said method comprising the steps of:
  • the inflammatory bowel disease is ulcerative colitis and the treatment comprises or consists of mesalamine administration, corticosteroid administration, multimatrix administration, budesonide administration, infliximab administration, adalimumab administration, golimumab administration, vedolizumab
  • the inflammatory bowel disease is Crohn's disease and the treatment comprises or consists of corticosteroid administration, anti-tumor necrosis factor drug administration, such as infliximab, adalimumab and certolizumab pegol, surgery, or a combination thereof.
  • a method of identifying a group of genomic regions having different expression profiles in a healthy subject and in a subject suffering from inflammatory bowel disease comprising the steps of:
  • transcripts and at least part of the second set of transcripts
  • RNA sequencing or 5'-RNA sequencing of capped RNAs (CAGE).
  • CAGE capped RNAs
  • the sample is a pinch biopsy, for example a sample from the colon, preferably from the descending colon.
  • kits of parts comprising:
  • a computer implemented method for automatically determining whether a subject is healthy or suffers from an inflammatory bowel disease comprising the steps of:
  • the markers are as defined in any one of the preceding items, and wherein the expression profile represents the expression levels of the at least 2 markers together in said subject, the first expression signature represents the average expression levels of the at least 2 markers together in a group of at least 20 healthy subjects, and the second expression signature represents the average expression levels of the at least 2 markers together in a group of subjects suffering from an inflammatory bowel disease;
  • the method determines that the subject is healthy
  • a computer implemented method for determining whether a subject suffers from ulcerative colitis or from Crohn's disease comprising the steps of: i) comparing the expression profile of at least 2 markers in a sample obtained from said subject with a first reference profile representative of healthy subjects, with a second reference profile representative of subjects suffering from ulcerative colitis and with a third reference profile representative of subjects suffering from Crohn's disease, wherein the markers are as defined in any one of the preceding items, and wherein the expression profile represents the expression levels of the at least 2 markers together in said subject, the first reference profile represents the average expression levels of the at least 2 markers together in a group of at least 20 healthy subjects, the second reference profile represents the average expression levels of the at least 2 markers together in a group of subjects suffering from ulcerative colitis and the third reference profile represents the average expression levels of the at least 2 markers together in a group of subjects suffering from Crohn's disease;
  • a system comprising a computer and a computer implemented method

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Abstract

La présente invention concerne des régions génomiques qui sont des marqueurs utiles pour déterminer si un sujet souffre d'une maladie intestinale inflammatoire, telle que la rectocolite hémorragique ou la maladie de Crohn, ou est sain. L'invention concerne également des amorces utiles pour mesurer des niveaux d'expression desdits marqueurs, ainsi que des procédés mis en œuvre par ordinateur.
PCT/EP2018/068244 2017-07-07 2018-07-05 Marqueurs pour diagnostiquer des maladies intestinales inflammatoires WO2019008093A1 (fr)

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Citations (2)

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WO2001029269A2 (fr) * 1999-10-21 2001-04-26 Case Western Reserve University Profilage de l'expression genetique d'une affection intestinale inflammatoire
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